Deoxygenation and molecular structural modification is a critical step before the practical application of triglycerides in aviation biofuels. For low quality waste triglycerides with high viscosity, traditional way of direct hydrogenation usually has problems such as catalyst deactivation and pipe clogging. Herein, we demonstrate a facile catalytic biorefinery process for high viscosity waste triglycerides for the production of aviation biofuels via a two-step catalytic conversion. Several typical plant oils (soybean and rubber seed oils) and waste triglycerides (waste cooking and acidified plant oils) are tested, which indicate that this approach is widely applicable, and can be used to produce aviation range products, linear hydrocarbons, at high yields (55%–60%), accompanied by a diesel range fuel of 15%–40% by adjusting the operation parameters. The aviation range hydrocarbons are further catalyzed by an Ni/ZSM-5 catalyst to achieve aromatization and hydrogenation in a one-pot synthesis. Three dominant components existing in aviation fuels, including chain hydrocarbons, aromatics and cycloalkanes, can be obtained, which present the same physical-chemical properties and components as petroleum-based aviation fuels. The proportion of the three main components can be modified by the amount of molecular sieve catalyst and the initial pressure of H2, in order to meet the requirements of variable-grade aviation fuels. Overall, a catalytic refining process of decarboxylation and molecular structural modification of low quality waste triglycerides for the entire/total substitution of petroleum aviation fuels from waste triglyceride is reported.